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- PDB-5qu4: Crystal Structure of swapped human Nck SH3.1 domain, 1.05A, ortho... -

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Basic information

Entry
Database: PDB / ID: 5qu4
TitleCrystal Structure of swapped human Nck SH3.1 domain, 1.05A, orthorhombic form I
ComponentsCytoplasmic protein NCK1Cytoplasm
KeywordsSIGNALING PROTEIN / SH3 DOMAIN / ADAPTOR / PEPTIDE BINDING / DOMAIN SWAP
Function / homology
Function and homology information


positive regulation of cap-dependent translational initiation / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / eukaryotic initiation factor eIF2 binding / positive regulation of peptidyl-serine dephosphorylation / protein phosphatase type 1 complex / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of cap-independent translational initiation / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity ...positive regulation of cap-dependent translational initiation / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / eukaryotic initiation factor eIF2 binding / positive regulation of peptidyl-serine dephosphorylation / protein phosphatase type 1 complex / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of cap-independent translational initiation / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity / vesicle membrane / signal complex assembly / Activation of RAC1 / Nephrin family interactions / DCC mediated attractive signaling / lamellipodium assembly / RHOV GTPase cycle / positive regulation of actin filament polymerization / protein kinase inhibitor activity / negative regulation of PERK-mediated unfolded protein response / antiviral innate immune response / RHOU GTPase cycle / Generation of second messenger molecules / RHO GTPases Activate WASPs and WAVEs / ephrin receptor signaling pathway / signaling adaptor activity / negative regulation of peptidyl-serine phosphorylation / regulation of cell migration / negative regulation of insulin receptor signaling pathway / positive regulation of T cell proliferation / response to endoplasmic reticulum stress / ephrin receptor binding / T cell activation / molecular condensate scaffold activity / Downstream signal transduction / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / FCGR3A-mediated phagocytosis / PKR-mediated signaling / receptor tyrosine kinase binding / Regulation of actin dynamics for phagocytic cup formation / positive regulation of neuron projection development / VEGFA-VEGFR2 Pathway / cell migration / cell-cell junction / signaling receptor complex adaptor activity / protein-macromolecule adaptor activity / Potential therapeutics for SARS / ribosome / cadherin binding / protein domain specific binding / signaling receptor binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nck1, SH3 domain 1 / Nck1, SH3 domain 2 / Nck1, SH3 domain 3 / Nck1, SH2 domain / Cytoplasmic protein NCK / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...Nck1, SH3 domain 1 / Nck1, SH3 domain 2 / Nck1, SH3 domain 3 / Nck1, SH2 domain / Cytoplasmic protein NCK / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
SH2/SH3 adapter protein NCK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsRudolph, M.G.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Small molecule AX-024 reduces T cell proliferation independently of CD3ε/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain.
Authors: Richter, K. / Rufer, A.C. / Muller, M. / Burger, D. / Casagrande, F. / Grossenbacher, T. / Huber, S. / Hug, M.N. / Koldewey, P. / D'Osualdo, A. / Schlatter, D. / Stoll, T. / Rudolph, M.G.
History
DepositionDec 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Structure summary / Category: pdbx_deposit_group
Item: _pdbx_deposit_group.group_description / _pdbx_deposit_group.group_type
Revision 1.2Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Database references / Refinement description / Category: citation / pdbx_initial_refinement_model / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic protein NCK1
B: Cytoplasmic protein NCK1
C: Cytoplasmic protein NCK1
D: Cytoplasmic protein NCK1


Theoretical massNumber of molelcules
Total (without water)41,1984
Polymers41,1984
Non-polymers00
Water5,549308
1
A: Cytoplasmic protein NCK1
C: Cytoplasmic protein NCK1


Theoretical massNumber of molelcules
Total (without water)20,5992
Polymers20,5992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-26 kcal/mol
Surface area6860 Å2
MethodPISA
2
B: Cytoplasmic protein NCK1
D: Cytoplasmic protein NCK1


Theoretical massNumber of molelcules
Total (without water)20,5992
Polymers20,5992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-19 kcal/mol
Surface area7340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.213, 57.482, 85.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cytoplasmic protein NCK1 / Cytoplasm / NCK adaptor protein 1 / Nck-1 / SH2/SH3 adaptor protein NCK-alpha


Mass: 10299.410 Da / Num. of mol.: 4 / Fragment: SH3 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCK1, NCK / Plasmid: PET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16333
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.56 Å3/Da / Density % sol: 20.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M KSCN, 30% PEG-MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→47.73 Å / Num. obs: 120355 / % possible obs: 100 % / Redundancy: 6.78 % / Biso Wilson estimate: 18.345 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.069 / Χ2: 0.836 / Net I/σ(I): 9.38 / Num. measured all: 815521 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.05-1.086.1954.3370.3254405878787820.1764.73899.9
1.08-1.116.2853.020.5254116861286110.3293.295100
1.11-1.146.0241.9290.8350216833983360.522.113100
1.14-1.176.5671.4951.1653359812881250.6541.624100
1.17-1.216.6671.2261.4552495787678740.7421.331100
1.21-1.256.6340.9581.8750601762976270.8021.041100
1.25-1.36.470.732.3547657736773660.870.795100
1.3-1.367.1870.5563.350889708170810.9470.599100
1.36-1.427.2820.3914.6849611681468130.9650.421100
1.42-1.487.2420.2886.447131651065080.9770.311100
1.48-1.576.7730.2028.6542069621162110.9860.219100
1.57-1.667.5540.1512.2744582590259020.9920.161100
1.66-1.777.5480.1111641893555055500.9950.12100
1.77-1.927.3420.08220.9638001517651760.9970.089100
1.92-2.16.6490.0625.9931908480047990.9970.065100
2.1-2.357.0110.05329.6330359433143300.9980.057100
2.35-2.717.1930.04932.8827707385238520.9980.053100
2.71-3.326.7580.04334.9122309330233010.9990.046100
3.32-4.76.1840.0435.3116004259125880.9980.04399.9
4.7-47.736.7030.0436.7410209152715230.9940.04399.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.05→47.73 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.343 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 3966 5 %RANDOM
Rwork0.1532 ---
obs0.1549 74603 65.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.39 Å2 / Biso mean: 17.97 Å2 / Biso min: 5.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å2-0 Å2
2---0.15 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.05→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 0 308 2244
Biso mean---27.67 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022179
X-RAY DIFFRACTIONr_bond_other_d0.0020.022033
X-RAY DIFFRACTIONr_angle_refined_deg2.1861.9282969
X-RAY DIFFRACTIONr_angle_other_deg1.09934744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56424.516124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36615433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9251520
X-RAY DIFFRACTIONr_chiral_restr0.150.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022437
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02475
X-RAY DIFFRACTIONr_rigid_bond_restr3.90234212
X-RAY DIFFRACTIONr_sphericity_free21.9745190
X-RAY DIFFRACTIONr_sphericity_bonded11.54854270
LS refinement shellResolution: 1.052→1.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 7 -
Rwork0.253 144 -
all-151 -
obs--1.72 %

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